It's a problem that we all share and there's really no "right" answer as to what you should do about them. It's true that deleting them isn't necessarily the most productive thing to do because that's just losing data - then again - since Marketo uses email as the unique identifier, you're relying on manual processes such as merging leads or updating lead information to fill in your gaps.
There are companies out there that will enrich your data and try to fill that gap, and Marketo has some partners on Launchpoint for achieving such a goal.
One thing I've seen adopted as a practice by some marketing teams and was really fond of, was actually using this data enhancement as a metric to measure the amount of value being provided by data enrichment tools. It gives you a way of seeing the value of something (data) which is otherwise often very hard to measure because in this case it has a binary metric to it (no email = bad, email = good... well... sometimes ).
Hope this helps,